Link Search Menu Expand Document

RO-Crate in use

These applications use or expose RO-Crates to describe Data, Datasets and Workflows:

WorkflowHub

WorkflowHub imports and exports Workflow RO-Crates, using it as an exchange format. They are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.

LifeMonitor

LifeMonitor uses RO-Crate as an exchange format for describing test suites associated with workflows. To this end, the LifeMonitor team is developing an extension to the Workflow RO-Crate specification to support the inclusion of metadata related to the testing of computational workflows stored in the crate.

Arkisto

Arkisto uses RO-Crate for packaging data objects in the 3 uses cases described below.

As part of these use-cases they have been developing or enhancing their tooling to facilitate their use of RO-Crate

Modern PARADISEC

Modern PARADISEC demonstrates the use of RO-Crate to describe the collections and items and store those items within an OCFL system. The demonstrator includes an elastic search service and a webserver but the key feature is that the it keeps working with only the filesystem and a webserver.

UTS Research Data Repository

The UTS Data Repository UTS Research Data Repository is a searchable portal for discovering and accessing public datasets by UTS researchers. Datasets are described with RO-Crates and published either through the University’s institutional research data management system or direct import from research storage devices for very large datasets.

UTS Cultural Datasets

The UTS Cultural Datasets project is collaborating with Humanities and Social Science (HASS) researchers and is re-using existing UTS Data infrastructure to build interactive services that allow people to use the data. They make use of RO-Crate to be able to directly transfer data and mappings to the Expert Nation database.

Workflow Execution Service (WfExS)

WfExS-backend is a high-level workflow execution command line program that consumes and creates RO-Crates, focusing on the interconnection of content-sensitive research infrastructures for handling sensitive human data analysis scenarios. WfExS-backend delegates workflow execution of existing workflow engines, and it is designed to facilitate more secure and reproducible workflow executions to promote analysis reproducibility and replicability. Secure executions are achieved using FUSE encrypted directories for non-disclosable inputs, intermediate workflow execution results and output files.

RO-Crates are, indeed, an element of knowledge transfer between repeated workflow executions. WfExS-backend stores all the gathered details, output metadata and execution provenance in the output RO-Crate to achieve future reproducible executions. Final execution results can be encrypted with crypt4gh GA4GH standard using the public keys of the target researchers or destination, so the results can be safely moved outside the execution environments through unsecured networks and storages.

ROHub

ROHub is a solution for the storage, lifecycle management and preservation of scientific work and operational processes via research objects. It makes these resources available to others, allows to publish and release them through a DOI, and allows to discover and reuse pre-existing scientific knowledge.

ROHub imports and exports RO-Crates, using it as an exchange format, particularly for Earth Science data cubes following the RELIANE RO-Crate profile.

Research Object Composer

Research Object Composer is a REST API for gradually building and depositing Research Objects according to a pre-defined profile. It uses JSON as an intermediate format and modified JSON schemas to define a Profile (RO-Crate support alpha)

Machine-actionable data management plans

RDA maDMP Mapper and [Ro-Crate_2ma-DMP](https://github.com/BrennerG/Ro-Crate_2_ma-DMP/tree/r2d) can convert between machine-actionable data management plans (maDMP) and RO-Crate. See https://doi.org/10.4126/frl01-006423291 for details.

DataPlant

DataPlant is implementing Annotated Research Context (ARC), an RO-Crate profile that combines the Investigation Study Assay model (ISA) and the Common Workflow Language (CWL) to capture a range from single experimental setups to complex experimental designs.

In ARC, files are managed in a git repository with a fixed structure following the ISA model, in addition to metadata in an Excel spreadsheet. The arcCommander tool can help with managing this structure, while the tool arc–to-roc can inspect the structure to generate an RO-Crate metadata file.


Table of contents